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Hendricks NG, Bhosale SD, Keoseyan AJ, Ortiz J, Stotland A, Seyedmohammad S, Nguyen CDL, Bui J, Moradian A, Mockus SM, Van Eyk JE. An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591396. [PMID: 38712179 PMCID: PMC11071456 DOI: 10.1101/2024.04.26.591396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
This technical note presents a comprehensive proteomics workflow for the new combination of Orbitrap and Astral mass analyzers across biofluids, cells, and tissues. Central to our workflow is the integration of Adaptive Focused Acoustics (AFA) technology for cells and tissue lysis, to ensure robust and reproducible sample preparation in a high-throughput manner. Furthermore, we automated the detergent-compatible single-pot, solid-phase-enhanced sample Preparation (SP3) method for protein digestion, a technique that streamlines the process by combining purification and digestion steps, thereby reducing sample loss and improving efficiency. The synergy of these advanced methodologies facilitates a robust and high-throughput approach for cells and tissue analysis, an important consideration in translational research. This work disseminates our platform workflow, analyzes the effectiveness, demonstrates reproducibility of the results, and highlights the potential of these technologies in biomarker discovery and disease pathology. For cells and tissues (heart, liver, lung, and intestine) proteomics analysis by data-independent acquisition mode, identifications exceeding 10,000 proteins can be achieved with a 24-minute active gradient. In 200ng injections of HeLa digest across multiple gradients, an average of more than 80% of proteins have a CV less than 20%, and a 45-minute run covers ~90% of the expressed proteome. In plasma samples including naive, depleted, perchloric acid precipitated, and Seer nanoparticle captured, all with a 24-minute gradient length, we identified 87, 108, 96 and 137 out of 216 FDA approved circulating protein biomarkers, respectively. This complete workflow allows for large swaths of the proteome to be identified and is compatible across diverse sample types.
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Affiliation(s)
- Nathan G. Hendricks
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Santosh D. Bhosale
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Angel J. Keoseyan
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Josselin Ortiz
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Saeed Seyedmohammad
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Chi D. L. Nguyen
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Jonathan Bui
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Annie Moradian
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Susan M. Mockus
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
| | - Jennifer E Van Eyk
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90210, United States
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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2
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Starodubtseva NL, Tokareva AO, Volochaeva MV, Kononikhin AS, Brzhozovskiy AG, Bugrova AE, Timofeeva AV, Kukaev EN, Tyutyunnik VL, Kan NE, Frankevich VE, Nikolaev EN, Sukhikh GT. Quantitative Proteomics of Maternal Blood Plasma in Isolated Intrauterine Growth Restriction. Int J Mol Sci 2023; 24:16832. [PMID: 38069155 PMCID: PMC10706154 DOI: 10.3390/ijms242316832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Intrauterine growth restriction (IUGR) remains a significant concern in modern obstetrics, linked to high neonatal health problems and even death, as well as childhood disability, affecting adult quality of life. The role of maternal and fetus adaptation during adverse pregnancy is still not completely understood. This study aimed to investigate the disturbance in biological processes associated with isolated IUGR via blood plasma proteomics. The levels of 125 maternal plasma proteins were quantified by liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM MS) with corresponding stable isotope-labeled peptide standards (SIS). Thirteen potential markers of IUGR (Gelsolin, Alpha-2-macroglobulin, Apolipoprotein A-IV, Apolipoprotein B-100, Apolipoprotein(a), Adiponectin, Complement C5, Apolipoprotein D, Alpha-1B-glycoprotein, Serum albumin, Fibronectin, Glutathione peroxidase 3, Lipopolysaccharide-binding protein) were found to be inter-connected in a protein-protein network. These proteins are involved in plasma lipoprotein assembly, remodeling, and clearance; lipid metabolism, especially cholesterol and phospholipids; hemostasis, including platelet degranulation; and immune system regulation. Additionally, 18 proteins were specific to a particular type of IUGR (early or late). Distinct patterns in the coagulation and fibrinolysis systems were observed between isolated early- and late-onset IUGR. Our findings highlight the complex interplay of immune and coagulation factors in IUGR and the differences between early- and late-onset IUGR and other placenta-related conditions like PE. Understanding these mechanisms is crucial for developing targeted interventions and improving outcomes for pregnancies affected by IUGR.
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Affiliation(s)
- Natalia L. Starodubtseva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
- Moscow Institute of Physics and Technology, 141700 Moscow, Russia
| | - Alisa O. Tokareva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
| | - Maria V. Volochaeva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
| | - Alexey S. Kononikhin
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
| | - Alexander G. Brzhozovskiy
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
| | - Anna E. Bugrova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Angelika V. Timofeeva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
| | - Evgenii N. Kukaev
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Victor L. Tyutyunnik
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
| | - Natalia E. Kan
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
| | - Vladimir E. Frankevich
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
- Laboratory of Translational Medicine, Siberian State Medical University, 634050 Tomsk, Russia
| | - Evgeny N. Nikolaev
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Gennady T. Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; (A.O.T.); (M.V.V.); (A.S.K.); (A.G.B.); (A.E.B.); (A.V.T.); (E.N.K.); (V.L.T.); (N.E.K.); (V.E.F.); (G.T.S.)
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3
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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4
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Abdelkader Y, Perez-Davalos L, LeDuc R, Zahedi RP, Labouta HI. Omics approaches for the assessment of biological responses to nanoparticles. Adv Drug Deliv Rev 2023; 200:114992. [PMID: 37414362 DOI: 10.1016/j.addr.2023.114992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.
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Affiliation(s)
- Yasmin Abdelkader
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St., Cairo 12622, Egypt
| | - Luis Perez-Davalos
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada
| | - Richard LeDuc
- Children's Hospital Research Institute of Manitoba, 513 - 715 McDermot Av. W, Winnipeg, Manitoba R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada; Department of Internal Medicine, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; CancerCare Manitoba Research Institute, 675 McDermot Av., Manitoba R3E 0V9, Canada
| | - Hagar I Labouta
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario M5S 3M2, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada; Faculty of Pharmacy, Alexandria University, 1 Khartoum Square, Azarita, Alexandria, Egypt, 21521.
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5
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Mohammed Y, Goodlett D, Borchers CH. Absolute Quantitative Targeted Proteomics Assays for Plasma Proteins. Methods Mol Biol 2023; 2628:439-473. [PMID: 36781801 DOI: 10.1007/978-1-0716-2978-9_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Preclinical and clinical trials require rapid, precise, and multiplexed analytical methods to characterize the complex samples and to allow high-throughput biomarker monitoring with low consumption of sample material. Targeted proteomics has been used to address these challenges when quantifying protein abundances in complex biological matrices. In many of these studies, blood plasma is collected either as the main research or diagnostic sample or in combination with other specimens. Mass spectrometry (MS)-based targeted proteomics using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) with stable isotope-labeled internal standard (SIS) peptides allows robust characterization of blood plasma protein via absolute quantification. Compared to other commonly used technologies like enzyme-linked immunosorbent assay (ELISA), targeted proteomics is faster, more sensitive, and more cost-effective. Here we describe a protocol for the quantification of proteins in blood plasma using targeted MRM proteomics with heavy-labeled internal standards. The 270-protein panel allows rapid and robust absolute quantitative proteomic characterization of blood plasma in a 1 h gradient. The method we describe here works for non-depleted plasma, which makes it simple and easy to implement. Moreover, the protocol works with the two most commonly used blood plasma collection methods used in practice, namely, either K2EDTA or sodium citrate as anticoagulants.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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6
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Mohammed Y, Goodlett D, Borchers CH. Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics. Methods Mol Biol 2023; 2628:557-577. [PMID: 36781806 DOI: 10.1007/978-1-0716-2978-9_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In targeted proteomics experiments, selecting the appropriate proteotypic peptides as surrogate for the target protein is a crucial pre-acquisition step. This step is largely a bioinformatics exercise that involves integrating information on the peptides and proteins and using various software tools and knowledgebases. We present here a few resources that automate and simplify the selection process to a great degree. These tools and knowledgebases were developed primarily to streamline targeted proteomics assay development and include PeptidePicker, PeptidePickerDB, MRMAssayDB, MouseQuaPro, and PeptideTracker. We have used these tools to develop and document thousands of targeted proteomics assays, many of them for plasma proteins with focus on human and mouse. An important aspect in all these resources is the integrative approach on which they are based. Using these tools in the first steps of designing a singleplexed or multiplexed targeted proteomic experiment can reduce the necessary experimental steps tremendously. All the tools and knowledgebases we describe here are Web-based and freely accessible so scientists can query the information conveniently from the browser. This chapter provides an overview of these software tools and knowledgebases, their content, and how to use them for targeted plasma proteomics. We further demonstrate how to use them with the results of the HUPO Human Plasma Proteome Project to produce a new database of 3.8 k targeted assays for known human plasma proteins. Upon experimental validation, these assays should help in the further quantitative characterizing of the plasma proteome.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, ZA, Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada. .,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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7
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Pauletti BA, Granato DC, M Carnielli C, Câmara GA, Normando AGC, Telles GP, Leme AFP. Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics. J Proteome Res 2023; 22:539-545. [PMID: 36480281 DOI: 10.1021/acs.jproteome.2c00585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The selection of a suitable proteotypic peptide remains a challenge for designing a targeted quantitative proteomics assay. Although the criteria are well-established in the literature, the selection of these peptides is often performed in a subjective and time-consuming manner. Here, we have developed a practical and semiautomated workflow implemented in an open-source program named Typic. Typic is designed to run in a command line and a graphical interface to help selecting a list of proteotypic peptides for targeted quantitation. The tool combines the input data and downloads additional data from public repositories to produce a file per protein as output. Each output file includes relevant information to the selection of proteotypic peptides organized in a table, a colored ranking of peptides according to their potential value as targets for quantitation and auxiliary plots to assist users in the task of proteotypic peptides selection. Taken together, Typic leads to a practical and straightforward data extraction from multiple data sets, allowing the identification of most suitable proteotypic peptides based on established criteria, in an unbiased and standardized manner, ultimately leading to a more robust targeted proteomics assay.
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Affiliation(s)
- Bianca A Pauletti
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Daniela C Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Carolina M Carnielli
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Guilherme A Câmara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Ana Gabriela C Normando
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Guilherme P Telles
- Instituto de Computação, Universidade Estadual de Campinas (UNICAMP), Campinas, 13083-852 São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
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8
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Wang Z, Cryar A, Lemke O, Tober-Lau P, Ludwig D, Helbig ET, Hippenstiel S, Sander LE, Blake D, Lane CS, Sayers RL, Mueller C, Zeiser J, Townsend S, Demichev V, Mülleder M, Kurth F, Sirka E, Hartl J, Ralser M. A multiplex protein panel assay for severity prediction and outcome prognosis in patients with COVID-19: An observational multi-cohort study. EClinicalMedicine 2022; 49:101495. [PMID: 35702332 PMCID: PMC9181834 DOI: 10.1016/j.eclinm.2022.101495] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Global healthcare systems continue to be challenged by the COVID-19 pandemic, and there is a need for clinical assays that can help optimise resource allocation, support treatment decisions, and accelerate the development and evaluation of new therapies. METHODS We developed a multiplexed proteomics assay for determining disease severity and prognosis in COVID-19. The assay quantifies up to 50 peptides, derived from 30 known and newly introduced COVID-19-related protein markers, in a single measurement using routine-lab compatible analytical flow rate liquid chromatography and multiple reaction monitoring (LC-MRM). We conducted two observational studies in patients with COVID-19 hospitalised at Charité - Universitätsmedizin Berlin, Germany before (from March 1 to 26, 2020, n=30) and after (from April 4 to November 19, 2020, n=164) dexamethasone became standard of care. The study is registered in the German and the WHO International Clinical Trials Registry (DRKS00021688). FINDINGS The assay produces reproducible (median inter-batch CV of 10.9%) absolute quantification of 47 peptides with high sensitivity (median LLOQ of 143 ng/ml) and accuracy (median 96.8%). In both studies, the assay reproducibly captured hallmarks of COVID-19 infection and severity, as it distinguished healthy individuals, mild, moderate, and severe COVID-19. In the post-dexamethasone cohort, the assay predicted survival with an accuracy of 0.83 (108/130), and death with an accuracy of 0.76 (26/34) in the median 2.5 weeks before the outcome, thereby outperforming compound clinical risk assessments such as SOFA, APACHE II, and ABCS scores. INTERPRETATION Disease severity and clinical outcomes of patients with COVID-19 can be stratified and predicted by the routine-applicable panel assay that combines known and novel COVID-19 biomarkers. The prognostic value of this assay should be prospectively assessed in larger patient cohorts for future support of clinical decisions, including evaluation of sample flow in routine setting. The possibility to objectively classify COVID-19 severity can be helpful for monitoring of novel therapies, especially in early clinical trials. FUNDING This research was funded in part by the European Research Council (ERC) under grant agreement ERC-SyG-2020 951475 (to M.R) and by the Wellcome Trust (IA 200829/Z/16/Z to M.R.). The work was further supported by the Ministry of Education and Research (BMBF) as part of the National Research Node 'Mass Spectrometry in Systems Medicine (MSCoresys)', under grant agreements 031L0220 and 161L0221. J.H. was supported by a Swiss National Science Foundation (SNSF) Postdoc Mobility fellowship (project number 191052). This study was further supported by the BMBF grant NaFoUniMedCOVID-19 - NUM-NAPKON, FKZ: 01KX2021. The study was co-funded by the UK's innovation agency, Innovate UK, under project numbers 75594 and 56328.
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Affiliation(s)
- Ziyue Wang
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Adam Cryar
- Inoviv, Mappin House, 4 Winsley St, London, United Kingdom
| | - Oliver Lemke
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Daniela Ludwig
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Elisa Theresa Helbig
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Leif-Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Berlin Institute of Health at the Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | | | | | - Christoph Mueller
- Agilent Technologies Sales & Services GmbH & Co. KG, Waldbronn, Germany
| | - Johannes Zeiser
- Agilent Technologies Sales & Services GmbH & Co. KG, Waldbronn, Germany
| | - StJohn Townsend
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Vadim Demichev
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Michael Mülleder
- Core Facility – High-Throughput Mass Spectrometry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, and Department of Medicine I, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Corresponding author: Florian Kurth, Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Augustenburger Platz 1, 13353 Berlin, Germany. Tel.: +49 (0)30 450 553052.
| | - Ernestas Sirka
- Inoviv, Mappin House, 4 Winsley St, London, United Kingdom
- Corresponding author: Ernestas Sirka, Inoviv, Mappin House, 4 Winsley St, London W1W 8HF, United Kingdom, Tel.: +44 (0)20 3239 0178.
| | - Johannes Hartl
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
- Corresponding author: Johannes Hartl, Charité – Universitätsmedizin Berlin, Department of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany. Tel.: +49 (0)30 450 528317.
| | - Markus Ralser
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Corresponding author: Markus Ralser, Charité – Universitätsmedizin Berlin, Department of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany. Tel.: +49 (0)30 450 528141
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Mohammed Y, Touw CE, Nemeth B, van Adrichem RA, Borchers CH, Rosendaal FR, van Vlijmen BJ, Cannegieter SC. Targeted proteomics for evaluating risk of venous thrombosis following traumatic lower-leg injury or knee arthroscopy. J Thromb Haemost 2022; 20:684-699. [PMID: 34919779 PMCID: PMC9303526 DOI: 10.1111/jth.15623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/22/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Patients with lower-leg cast immobilization and patients undergoing knee arthroscopy have an increased risk of venous thrombosis (VT). Guidelines are ambiguous about thromboprophylaxis use, and individual risk factors for developing VT are often ignored. To assist in VT risk stratification and guide thromboprophylaxis use, various prediction models have been developed. These models depend largely on clinical factors and provide reasonably good C-statistics of around 70%. We explored using protein levels in blood plasma measured by multiplexed quantitative targeted proteomics to predict VT. Our aim was to assess whether a VT risk prediction model based on absolute plasma protein quantification is possible. METHODS We used internal standards to quantify proteins in less than 10 μl plasma. We measured 270 proteins in samples from patients scheduled for knee arthroscopy or with lower-leg cast immobilization. The two prospective POT-(K)CAST trails allow complementary views of VT signature in blood, namely pre and post trauma, respectively. From approximately 3000 patients, 31 patients developed VT who were included and matched with double the number of controls. RESULTS Top discriminating proteins between cases and controls included APOC3, APOC4, APOC2, ATRN, F13B, and F2 in knee arthroscopy patients and APOE, SERPINF2, B2M, F13B, AFM, and C1QC in patients with lower-leg cast. A logistic regression model with cross-validation resulted in C-statistics of 88.1% (95% CI: 85.7-90.6%) and 79.6% (95% CI: 77.2-82.0%) for knee arthroscopy and cast immobilization groups respectively. CONCLUSIONS Promising C-statistics merit further exploration of the value of proteomic tests for predicting VT risk upon additional validation.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenThe Netherlands
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaBritish ColumbiaCanada
| | - Carolina E. Touw
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Orthopaedic SurgeryLeiden University Medical CenterLeidenThe Netherlands
| | - Banne Nemeth
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Orthopaedic SurgeryLeiden University Medical CenterLeidenThe Netherlands
| | - Raymond A. van Adrichem
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Orthopaedic SurgeryLeiden University Medical CenterLeidenThe Netherlands
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreSegal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyJewish General Hospital, McGill UniversityMontrealQuebecCanada
- Department of Data Intensive Science and EngineeringSkolkovo Institute of Science and TechnologySkolkovo Innovation CenterMoscowRussia
| | - Frits R. Rosendaal
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Bart J. van Vlijmen
- Einthoven Laboratory for Experimental Vascular MedicineDepartment of Internal MedicineDivision of Thrombosis & HemostasisLeiden University Medical CenterLeidenThe Netherlands
| | - Suzanne C. Cannegieter
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Einthoven Laboratory for Experimental Vascular MedicineDepartment of Internal MedicineDivision of Thrombosis & HemostasisLeiden University Medical CenterLeidenThe Netherlands
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10
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Schmidt A, Schreiner D. Quantitative Detection of Protein Splice Variants by Selected Reaction Monitoring (SRM) Mass Spectrometry. Methods Mol Biol 2022; 2537:231-246. [PMID: 35895268 DOI: 10.1007/978-1-0716-2521-7_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular diversification of the cellular proteome through alternative splicing has emerged as an important biological principle. However, the lack of tools to specifically detect and quantify proteoforms (Smith et al., Nat Methods 10:186-187, 2013) is a major impediment to functional studies. Recently, biological mass spectrometry (MS) has undergone impressive advances (Mann, Nat Rev Mol Cell Biol 17:678, 2016), including the generation of a highly diverse set of biological applications (Aebersold and Mann, Nature 537:347-355, 2016), and has demonstrated to be an essential tool to address many biological questions (Savitski et al., Science 346:1255784, 2014; Rinner et al., Nat Methods 5:315-318, 2008). In particular, targeted LC-MS, with its high selectivity and specificity, is ideally suited for the precise and sensitive quantification of specific proteins and their proteoforms (Picotti and Aebersold, Nat Methods 9:555-566, 2012). We describe in detail the application of this workflow applied to dissect the molecular diversity of the synaptic adhesion proteins and their splicing-derived proteoforms (Schreiner et al., Elife 4:e07794, 2015).
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11
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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12
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Lill JR, Mathews WR, Rose CM, Schirle M. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics 2021; 18:503-526. [PMID: 34320887 DOI: 10.1080/14789450.2021.1962300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. AREAS COVERED Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. EXPERT OPINION Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.
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Affiliation(s)
- Jennie R Lill
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - William R Mathews
- OMNI Department, Genentech Inc. 1 DNA Way, South San Francisco, CA, USA
| | - Christopher M Rose
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - Markus Schirle
- Chemical Biology and Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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13
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Tidmore A, Dutta SM, Fesshaye AS, Russell WK, Duncan VD, Britten RA. Space Radiation-Induced Alterations in the Hippocampal Ubiquitin-Proteome System. Int J Mol Sci 2021; 22:ijms22147713. [PMID: 34299332 PMCID: PMC8304141 DOI: 10.3390/ijms22147713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022] Open
Abstract
Exposure of rodents to <20 cGy Space Radiation (SR) impairs performance in several hippocampus-dependent cognitive tasks, including spatial memory. However, there is considerable inter-individual susceptibility to develop SR-induced spatial memory impairment. In this study, a robust label-free mass spectrometry (MS)-based unbiased proteomic profiling approach was used to characterize the composition of the hippocampal proteome in adult male Wistar rats exposed to 15 cGy of 1 GeV/n 48Ti and their sham counterparts. Unique protein signatures were identified in the hippocampal proteome of: (1) sham rats, (2) Ti-exposed rats, (3) Ti-exposed rats that had sham-like spatial memory performance, and (4) Ti-exposed rats that impaired spatial memory performance. Approximately 14% (159) of the proteins detected in hippocampal proteome of sham rats were not detected in the Ti-exposed rats. We explored the possibility that the loss of the Sham-only proteins may arise as a result of SR-induced changes in protein homeostasis. SR-exposure was associated with a switch towards increased pro-ubiquitination proteins from that seen in Sham. These data suggest that the role of the ubiquitin-proteome system as a determinant of SR-induced neurocognitive deficits needs to be more thoroughly investigated.
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Affiliation(s)
- Alyssa Tidmore
- Department of Radiation Oncology, Eastern Virginia Medical School, 700 W. Olney Rd., Lewis Hall, Norfolk, VA 23507, USA; (A.T.); (A.S.F.); (V.D.D.)
- Department of Microbiology and Molecular Cell Biology; Eastern Virginia Medical School, Norfolk, VA 23507, USA;
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23507, USA
- Center for Integrative Neuroinflammatory and Inflammatory Diseases, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Sucharita M. Dutta
- Department of Microbiology and Molecular Cell Biology; Eastern Virginia Medical School, Norfolk, VA 23507, USA;
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Arriyam S. Fesshaye
- Department of Radiation Oncology, Eastern Virginia Medical School, 700 W. Olney Rd., Lewis Hall, Norfolk, VA 23507, USA; (A.T.); (A.S.F.); (V.D.D.)
- Department of Microbiology and Molecular Cell Biology; Eastern Virginia Medical School, Norfolk, VA 23507, USA;
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23507, USA
- Center for Integrative Neuroinflammatory and Inflammatory Diseases, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - William K. Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Vania D. Duncan
- Department of Radiation Oncology, Eastern Virginia Medical School, 700 W. Olney Rd., Lewis Hall, Norfolk, VA 23507, USA; (A.T.); (A.S.F.); (V.D.D.)
| | - Richard A. Britten
- Department of Radiation Oncology, Eastern Virginia Medical School, 700 W. Olney Rd., Lewis Hall, Norfolk, VA 23507, USA; (A.T.); (A.S.F.); (V.D.D.)
- Department of Microbiology and Molecular Cell Biology; Eastern Virginia Medical School, Norfolk, VA 23507, USA;
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23507, USA
- Center for Integrative Neuroinflammatory and Inflammatory Diseases, Eastern Virginia Medical School, Norfolk, VA 23507, USA
- Correspondence:
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